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Bioconductors:
We are pleased to announce the release of Bioconductor 2.2. This
release includes 35 new packages, and many improvements to existing
packages. There are now 260 package in Bioconductor 2.2. These
packages are compatible with R 2.7.0.
IMPORTANT: MAC OS USERS: the 'binary' builds currently available with
biocLite are not suitable for Tiger (OS X 10.4). We expect to have
Tiger-compatible builds within the next week. If you are using Tiger,
please refrain from migrating to R-2.7.0 until these binaries become
available, or use the 'type="source"' option to biocLite.
As a member of the Bioconductor community, you have contributed
greatly to this release. Perhaps you are a perplexed newcomer asking
for help on the Bioc mailing list. Perhaps you are an experienced user
seeking reproducible and advanced functionality. Or perhaps you are a
package developer helping others to make sound sense of their
data. Whatever your role, you've made Bioconductor the resource it is
today. We are especially grateful to package developers, to members of
the Bioconductor team in Seattle, and to those participants on the
Bioc mailing list who knowledgeably and patiently answer questions
large and small.
High-throughput genomic research is a dynamic and exciting field. It
is hard to predict what surprising packages are in store for future
Bioconductor releases. We anticipate continued integration with
diverse data sources, use of R's advanced graphics abilities, and
implementation of cutting edge research algorithms for the benefit of
all Bioconductor users. Short-read DNA resequencing technologies are
one area where growth seems almost certain.
We look forward to a vibrant release cycle!
Contents
========
* Getting Started With Bioconductor 2.2
* New and Re-introduced Packages
* Significant Changes to Annotation Packages
Getting Started With Bioconductor 2.2
=====================================
IMPORTANT: MAC USERS: see the important note above.
To install Bioconductor 2.2
1. Install R 2.7.0. Bioconductor 2.2 has been designed expressly for
this version of R.
2. Follow the instructions here:
http://bioconductor.org/download
Please visit http://bioconductor.org for details and downloads.
New and Re-introduced Packages
==============================
The following packages are new in this release of Bioconductor; visit
http://bioconductor.org/packages/release/Software.html
for links to all package descriptions.
AffyCompatible
Affymetrix GeneChip software compatibility
BAC
Bayesian Analysis of Chip-chip experiment
BCRANK
Predicting binding site consensus from ranked DNA sequences
BGmix
Bayesian models for differential gene expression
BiocCaseStudies
Support for the Bioconductor Case Studies Monograph
GEOmetadb
A compilation of metadata from NCBI GEO
GGBase
Infrastructure for genetics of gene expression (c) 2008 VJ Carey
GSEAlm
Linear Model Toolset for Gene Set Enrichment Analysis
GeneRfold
R for genes and sequences, using viennaRNA package (fold)
GeneSelector
GeneSelector
GenomeGraphs
Plotting genomic information from Ensembl
GraphAlignment
GraphAlignment
PCpheno
Phenotypes and cellular organizational units
RBioinf
Support for R for Bioinformatics Monograph
Rdisop
Decomposition of Isotopic Patterns
Rtreemix
Mutagenetic trees mixture models.
SLGI
Synthetic Lethal Genetic Interaction
XDE
A Bayesian hierarchical model for cross-study analysis of
differential gene expression
affyPara
Parallelized preprocessing methods for Affymetrix Oligonucleotide
Arrays
flowClust
Clustering for Flow Cytometry
flowQ
Qualitiy control for flow cytometry
flowUtils
Utilities for flow cytometry
gaga
GaGa hierarchical model for microarray data analysis
goProfiles
An R package for the statistical analysis of functional profiles
mdqc
Mahalanobis Distance Quality Control for microarrays
occugene
Functions for Multinomial Occupancy Distribution
plw
Probe level Locally moderated Weighted t-tests.
rtracklayer
R interface to genome browsers and their annotation tracks
snpMatrix
The snp.matrix and X.snp.matrix classes
xps
Methods for Processing and Analysis of Affymetrix Oligonucleotide
Arrays
yaqcaffy
Affymetrix expression data quality control and reproducibility
analysis
Additional packages have been re-introduced to the release branch:
GeneticsPed
Pedigree and genetic relationship functions
Rredland
Interface to redland RDF utilities
externalVector
Vector objects for R with external storage
stam
Structured Analysis of Microarray Data
Packages still present in the 'development' branch, but no longer in
the release, include BeadExplorer, GeneRfold, MCRestimate, and
SAGElyzer. Packages retired from Bioconductor include arrayMagic,
ChromoViz, GeneTS, iSNetwork, iSPlot, and RMAPPER.
Significant Changes to Annotation Packages
==========================================
Bioconductor 2.2 includes a large number of annotation
packages. Descriptions are available here:
http://bioconductor.org/packages/release/AnnotationData.html
New 'db' annotation packages replace their predecessors, e.g.,
hgu95av2.db replaces hgu95av2 . Both 'db' and original packages are
available in this release, but we anticipate that future releases will
only contain 'db' packages. Most db packages now contain Ensembl
accessions,
New 'organism' packages are available for several model organisms:
human,
org.Hs.eg.db; mouse, org.Mm.eg.db; rat, org.Rn.eg.db; yeast,
org.Sc.sgd.db; fly, org.Dm.eg.db; malaria, org.Pf.plasmo.db. Many of
these packages contain additional organism-specific annotations, e.g.,
flybase (Drosophila) or Jackson Laboratories (mouse) IDs.
New 'homology' packages summarize InParanoid homology data. Use these
and the organism packages to map between InParanoid and other IDS
IDs. Available homology packages include: human, hom.Hs.inp.db; mouse,
hom.Mm.inp.db; rat, hom.Rn.inp.db; yeast, hom.Sc.inp.db; fly,
hom.Dm.inp.db.
The PFAM package is available as PFAM.db
Custom CDF packages provided by Manhong Dai are not currently
available, but should be shortly.
Martin
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
